Did you know where she went?do you know where she went?哪个才对呢?

这要看你的语境.
但我感觉,应该是：
Do you know where she has gone --------这强调go的结果.
Do you know where she went?-------应该改写成 Do you know where she went yesterday -------需要加上go发生的确切时间.
------这一切都需要你的语感去理解.我只能说这麼多.